SMTL ID : 5jbi.1

Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC52 and manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x 6J8: [(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(4-methoxyphenyl)pentyl]phosphonic acid(Non-covalent)

6J8.1: 23 residues within 4Å: Chain A: K.139, D.165, S.166, E.167, S.203, S.204, G.205, G.206, W.230, M.232, I.236, S.240, N.245, K.246, E.249, C.272, H.275, P.292, D.293, M.294, P.297 Ligands: MN.2, GOL.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.292 Hydrogen bonds: A:K.139, A:S.166, A:S.204, A:G.205, A:G.206, A:S.240, A:N.245, A:K.246, A:D.293 Water bridges: A:K.246 pi-Stacking: A:W.230, A:W.230 6J8.11: 21 residues within 4Å: Chain B: K.139, D.165, S.166, E.167, S.203, S.204, G.205, G.206, W.230, M.232, I.236, S.240, N.245, K.246, E.249, H.275, P.292, D.293, M.294, P.297 Ligands: MN.12 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:P.292 Hydrogen bonds: B:K.139, B:S.166, B:S.204, B:S.204, B:S.204, B:G.205, B:G.206, B:N.245, B:K.246, B:D.293 Water bridges: B:S.203, B:S.203 pi-Stacking: B:W.230

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: K.139, D.165, S.166, E.167, E.249 Ligands: 6J8.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.165, A:E.167, A:E.167, A:E.249 MN.12: 5 residues within 4Å: Chain B: K.139, D.165, E.167, E.249 Ligands: 6J8.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.165, B:E.167, B:E.167, B:E.249

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: S.166, E.167, C.202, S.203, S.204, H.269, C.272, I.274, H.275 Ligands: 6J8.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.166, A:S.203, A:I.274, A:H.275

15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: E.265, V.266, Y.340 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.266, A:V.266 EDO.5: 3 residues within 4Å: Chain A: D.260, Y.261, N.262 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.261, A:N.262, A:N.262 EDO.6: 6 residues within 4Å: Chain A: S.191, I.196, N.197, V.259, D.260, D.263 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.197, A:D.260 EDO.7: 9 residues within 4Å: Chain A: V.143, S.144, A.145, G.146, F.147, N.347, F.348, P.350, T.351 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.143, A:F.147, A:T.351, A:T.351 EDO.8: 5 residues within 4Å: Chain A: L.330, K.337, Y.340, I.344 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.337 EDO.9: 6 residues within 4Å: Chain A: D.373, S.376, I.377, Q.380, I.415, H.419 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.376, A:Q.380 EDO.10: 1 residues within 4Å: Chain A: E.395 No protein-ligand interaction detected (PLIP) EDO.13: 10 residues within 4Å: Chain B: V.143, S.144, A.145, G.146, F.147, N.347, F.348, P.350, T.351, I.401 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.143, B:F.147, B:T.351 EDO.14: 4 residues within 4Å: Chain B: E.265, V.266, L.330, Y.340 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.266, B:V.266, B:Y.340 EDO.15: 5 residues within 4Å: Chain B: I.196, N.197, V.259, D.260, D.263 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.197, B:D.260 EDO.16: 8 residues within 4Å: Chain A: Q.173, C.174, L.175, D.176 Chain B: Q.173, C.174, L.175, D.176 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.173 Water bridges: B:D.176, B:D.176, B:D.176, A:Q.173, A:L.175 EDO.17: 2 residues within 4Å: Chain B: K.36, I.37 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.39 EDO.18: 3 residues within 4Å: Chain B: N.154, I.155, K.157 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.154, B:K.157 EDO.19: 3 residues within 4Å: Chain B: G.18, G.21, G.114 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.114 Water bridges: B:S.22, B:S.22 EDO.20: 3 residues within 4Å: Chain B: N.218, T.220, N.223 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.223, B:N.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sooriyaarachchi, S. et al., Targeting an Aromatic Hotspot in Plasmodium falciparum 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase with beta-Arylpropyl Analogues of Fosmidomycin. Chemmedchem (2016)

Release Date

2016-08-24

Peptides

1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic

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